Single atoms or residues can be deleted from the molecule using “Delete...” from the “Model/Fit/Refine”dialog. Pressing this button results in a new dialog, with the options of “Residue” (the default), “Atom” and “Hydrogen Atoms”. Now click on an atom in the graphics - the deleted object will be the whole residue of the atom if “Residue” was selected and just that atom if “Atom” was selected. Note that if a residue has an alternative conformation, then “Delete Residue” will delete only the conformation that matches that alternative conformation specifier of the clicked atom.
Only waters are deletable if the "Water" check button is active and waters are not deletable if the "Residue/Monomer" check button is active. This is to reduce mis-clicking.
To rotate the view when in “Delete Mode”, use Ctrl left-mouse.
If you want to delete multiple items you can use check the “Keep Delete Active” check-button on this dialog This will will keep the dialog open, ready for deletion of next item.